Simply nuking the shit out of everything wouldn’t really make for an interesting story.
It did for the Killing Star. Not nukes, but R-bombs which are probably the most insane WMD-s and unlike strangelet bombs actually feasible even at our current tech level. All you need is a light-sail and a big-ass solar-powered laser.
But, yeah, for dune:
Drop an active shield generator on your enemy position